State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest Agricultural and Forestry University, Yangling, Shaanxi, China.
PLoS One. 2012;7(9):e44510. doi: 10.1371/journal.pone.0044510. Epub 2012 Sep 5.
To ascertain genetic diversity, population structure and linkage disequilibrium (LD) among a representative collection of Chinese winter wheat cultivars and lines, 90 winter wheat accessions were analyzed with 269 SSR markers distributed throughout the wheat genome. A total of 1,358 alleles were detected, with 2 to 10 alleles per locus and a mean genetic richness of 5.05. The average genetic diversity index was 0.60, with values ranging from 0.05 to 0.86. Of the three genomes of wheat, ANOVA revealed that the B genome had the highest genetic diversity (0.63) and the D genome the lowest (0.56); significant differences were observed between these two genomes (P<0.01). The 90 Chinese winter wheat accessions could be divided into three subgroups based on STRUCTURE, UPGMA cluster and principal coordinate analyses. The population structure derived from STRUCTURE clustering was positively correlated to some extent with geographic eco-type. LD analysis revealed that there was a shorter LD decay distance in Chinese winter wheat compared with other wheat germplasm collections. The maximum LD decay distance, estimated by curvilinear regression, was 17.4 cM (r(2)>0.1), with a whole genome LD decay distance of approximately 2.2 cM (r(2)>0.1, P<0.001). Evidence from genetic diversity analyses suggest that wheat germplasm from other countries should be introduced into Chinese winter wheat and distant hybridization should be adopted to create new wheat germplasm with increased genetic diversity. The results of this study should provide valuable information for future association mapping using this Chinese winter wheat collection.
为了确定中国冬小麦品种和系的遗传多样性、群体结构和连锁不平衡（LD），利用分布在小麦全基因组的 269 个 SSR 标记，对 90 个冬小麦品系进行了分析。共检测到 1358 个等位基因，每个位点有 2-10 个等位基因，平均遗传丰富度为 5.05。平均遗传多样性指数为 0.60，范围从 0.05 到 0.86。在小麦的三个基因组中，方差分析表明 B 基因组的遗传多样性最高（0.63），D 基因组最低（0.56）；这两个基因组之间存在显著差异（P<0.01）。基于 STRUCTURE、UPGMA 聚类和主坐标分析，90 个中国冬小麦品系可分为三个亚群。来自 STRUCTURE 聚类的种群结构在一定程度上与地理生态型呈正相关。LD 分析表明，与其他小麦种质资源相比，中国冬小麦的 LD 衰减距离较短。用曲线回归估计的最大 LD 衰减距离为 17.4 cM（r(2)>0.1），全基因组 LD 衰减距离约为 2.2 cM（r(2)>0.1，P<0.001）。遗传多样性分析的证据表明，应该从其他国家引入小麦种质资源到中国冬小麦中，并采用远缘杂交来创造具有更高遗传多样性的新小麦种质资源。本研究的结果应为未来利用该中国冬小麦群体进行关联作图提供有价值的信息。
